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Ladeira et al. Microbiome Res Rep 2023;2:9 https://dx.doi.org/10.20517/mrr.2023.01 Page 7 of 15

Figure 1. Bifidobacterium-based gut microbiome partitions. (A) Model fit according to BIC; (B) distribution of subjects across the 7
partitions. Partition #7 consists of subjects for whom no Bifidobacterium was detected (no-Bif); (C) scaled contribution of each
Bifidobacterium species to each partition. Higher DMM model contributions are associated with a higher relative abundance of a
particular species. Species are ordered according to hierarchical clustering based on Euclidean distance. Gray indicates alpha parameters
-5
below 10 . More abundant species: B. longum to B. dentium and sub-dominant species: B. moukalabense to B. pseudolongum.

Figure 2. Distribution of subjects between Bifidobacterium-based gut microbiome partitions according to metadata (without recent
antibiotic intake). (A) Age category; (B) westernized lifestyle (adults); (C) health status (adults).

the cMD (> 1.000 adults) and extracted their Bifidobacterium partitions: (1) 1.098 individuals from the UK
enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study ; (2) 1.135
[12]
participants from the Dutch population-based cohort LifeLines-DEEP ; and (3) 800 individuals from an
[18]
Israeli cohort. All the identified partitions were detected in the three cohorts with different prevalences
[Supplementary Figure 5]. As for the cMD, the ado_lon and ado_lon_bif partitions were the most prevalent
(> 50%), and the no_Bif partition was the least prevalent (< 10%). We identified several partitions related to
Bifidobacterium composition in the adult gut microbiome. These differences were also observed when only
adults from the cMD were selected [Supplementary Table 1].

We then used DESeq2 to identify bacterial species for which abundance differed between partitions
(FDR < 0.05, Wald test) [Figure 3C]. We found that Bifidobacterium partitions enriched in both B. longum
and B. adolescentis (ado_lon, ado_lon_bif, and lon_ado_cat) shared common, differentially abundant
bacterial species compared to other partitions (contrasts on the left and right parts of the heatmap). The
ado_lon, ado_lon_bif, and lon_ado_cat partitions had a lower abundance of E. coli and a higher abundance
of several butyrate producers (Roseburia faecis, Coprococcus catus, C. eutactus, C. comes, and Eubacterium